Systematics Section / ASPT
Little, Damon , Stevenson, Dennis Wm. .
A comparison of algorithms for identification of specimens using DNA barcodes: examples from gymnosperms.
IN order to use DNA sequences for specimen identification (e.g., barcoding, fingerprinting) an algorithm to compare query sequences to a reference database is needed. Precision and accuracy of query sequence identification was estimated for hierarchical clustering (parsimony and neighbor joining), similarity methods (BLAST, BLAT, and megaBLAST), combined clustering/similarity methods (BLAST/parsimony and BLAST/neighbor joining), diagnostic methods (DNA–BAR and DOME ID), and a new method (ATIM) using publicly available gymnosperm nrITS 2 and plastid matK sequences as test data sets. We offer two novel alignment–free algorithmic solutions (DOME ID and ATIM) to identify query sequences for the purposes of DNA barcoding. On the test datasets, clustering methods performed the worst (perhaps due to alignment issues). Similarity methods, ATIM, DNA–BAR, and DOME ID all performed at approximately the same level. Almost all of the methods were able to accurately identify sequences to genus, however no method was able to accurately identify query sequences to species at a frequency that would be considered useful for routine specimen identification. Given the relative precision of the algorithms (median = 67% unambiguous), the low accuracy of species level identification observed could be ascribed to the lack of correspondence between patterns of allelic similarity and species delimitations. Application of DNA barcoding to sequences of CITES listed cycads (Cycadaceae) provides an example of the potential application of DNA barcoding to enforcement of conservation laws.
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1 - The New York Botanical Garden, Lewis B. and Dorothy Cullman Program for Molecular Systematic Studies, 200th St. & Southern Blvd., Bronx, New York, 10458-5126, USA
2 - New York Botanical Garden, Institute of Systematic Botany, 200Th Street & Southern Boulevard, Bronx, New York, 10458-5126, USA
Presentation Type: Oral Paper:Papers for Sections
Date: Monday, July 31st, 2006
Time: 4:15 PM